Error improper refpos+reflen
Issue #56
resolved
Hi there, I am trying to run jgi_summarize_bam_contig_depths on 6 different sorted.bam files. I get an error Error improper refpos+reflen. I have treated all my samples completely the same, so there should be no discrepancy due to using different reference genomes or BAM files coming from mapping reads against different reference databases. Is there a solution for this? I can create depth files for each sample separately without issues. thank you
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This issue indicates that at least one of your alignments extends past one of your reference sequences, and if you look at the read and contig for which the warning detailed the message and do the math then I presume you will come to the same conclusion. Please provide details if not. This may be a bug in the tool you used to perform the read to assembly mapping. As this is a common bug in a few mappers, this warning only has the effect of ignoring the reads that violate the mathematics of alignment and the result of the binning should be fine to use if this affects a small fraction of the data.
It may also be possible that your BAM files are not all mappings against the same assembly so their headers are different, though that should have triggered an error and you state that you have verified this is not the case. However, I am at a loss to explain why each individual bam file does not trigger this warning but the set of 6 together does.